If you experience this, PLEASE file a ticket with support so it is more readily visible to the devs.
It seems that the wood ducks on Askiy Ridge spook far too easily, regardless of being inside of a hunting structure. I tested at three different water bodies (both large beaver lakes in their home range, as well as a small pond in the southeastern corner of the map), as well as at various ranges between 15-50m with the same result, regardless of which hunting structure was used (including waterfowl blinds, layout blinds, and water layout blinds - a tripod as well for good measure). At any sort of range where birdshot is realistically able to consistently hit and kill them, they would go alert, then flee within a few seconds of landing; even reaching the alert status occasionally while passing directly overhead in the case of level 2-3 ducks. I have not tested northern pintails to the same degree, but they seem to be spooking under similar circumstances so I suspect they would behave much the same.
I don't believe this to be a purposeful change to waterfowl as a whole, given both species of goose as well as mallards on Askiy Ridge seem to be behaving as normal. although I have not yet tested ducks or geese on other maps.
This was all tested in a singleplayer setting.